Subject: Forcefield conversions

From: Mr Andrew D Allen <[email-masked]>
Date: Thu, 27 Jan 94 14:45:10 GMT

I could not reply directly to  <[email-masked]> so I am replying
to the net...

> Folks,
> 
> Does anyone out there have routines that do a reasonable conversion between
> atom types in different MM force fields. I'm particularly interested in
> baing able to take files that Sybyl puts out and convert them to something
> that CHARMm can read.
> 
Try this...

Title: A general approach for atom-type assignment and the
interconversion of molecular structure files..
Authors: T. J. O'Donnell, Shashidhar N. Rao, Konrad Koehler, Yvonne
C. Martin, Beverly Eccles.
Abstract: In molecular modeling projects which require the use of
several different computer programs, one encounters problems in
sharing data between programs. One difficult problem is the
conversion of atom types from one program's definition to another. A
second problem in the conversion of a polymer, such as a protein or
polynucleotide molecule, from a "general" program, which understands
molecules as a collection of atoms, to a polymer program, which
understands molecules as a collection of molecular fragments stored
in some library. We describe here a new method by which atom, types
are deduced from the environment of each atom. We use the Daylight
Chemical Information Systems library of programs to deduce the atom
types,  based only on atomic symbol, connectivity and formal charge
of each atom in the molecule. We also describe a method by which the
polypeptide nature and sequence of a molecule can be deduced from
minimal information about the atoms in the molecule. We have written
a computer program which demonstrates this method. This program
deduces atoms types for AMBER, GRIN/GRID, CHARMm, and ALOGP. It will
also produce input files for the AMBER/PREP fragment library
preparation program.
Keywords: Atom type conversions, SMILES, Daylight software.
Source: J. Comp. Chem, (1991), 12:2, 209 - 214.

Hope this is of use.
Andy.

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